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Project traces the genetic roots of the Earth's most ancient plants

Claude dePamphilis and colleagues trace the genetic roots of the Earth’s most ancient flowering plants.

Melissa Beattie-Moss

April 1, 2008

Project traces the genetic roots of the Earth's most ancient plants

Angiosperms, or flowering plants, are the most diverse group of plants on the planet with at least 260,000 species. They are also one of the most mysterious.

"The sudden appearance of flowers in the fossil record over 100 million years ago represents a great mystery," explains Claude dePamphilis. "Did the earliest flowers possess the full complement of genetic information needed to assemble a modern flower? What was the driver of the diversification of floral developmental pathways? Are there genes that have conserved functions throughout much of flowering plant history? These are the questions we're seeking to answer."

Six years ago, in order to try to solve this mystery, dePamphilis, professor of biology at Penn State, proposed a major study. With a grant of $7.4 million from the National Science Foundation, the Floral Genome Project was established at Penn State in 2001, with dePamphilis as co-director. "Our goal was to learn more about the evolutionary history of angiosperms by extracting and sequencing the genes expressed during early reproductive development from 15 different species of flowering plants and related species," he explains. The project has produced about 90 papers to date, including some major findings.

One fascinating finding, notes dePamphilis, was the discovery that modern gene sets from the earliest known flowering plant-a rare woody shrub from the South Pacific called Amborella -lacked evidence of past genome doubling, described as polyploidy events. The majority of ferns and flowering plants have the multiple sets of chromosomes indicative of polyploidization, dePamphilis explains, and such events are considered a powerful force in the evolution of angiosperm species.

Says dePamphilis, "It is very interesting to us that Amborella -the first branch off the tree of flowering plant life-was the only species we studied that lacked evidence for this kind of genome-wide duplication event. Our hypothesis is that flowering plants may have diversified by means of a very early polyploidy event that occurred either at the same time, or just after, the branching off of Amborella."

In addition to satisfying scientific curiosity, unraveling the mystery of angiosperm evolution may yield important advances in medicine and agriculture. "Plants in general-and these earliest branching lineages of angiosperms in particular-are a real pharmaceutical factory for unusual chemistries," says dePamphilis. "Through our projects, we're learning a lot about the genes that underlie an array of economically important agricultural traits in addition to flowers and fruits."

Adds dePamphilis with enthusiasm, "By identifying the specific functions of genes that regulate fruit development, we may learn how to manipulate them to help humankind. For instance, to understand the sets of genes that regulate fruit development in an avocado, we might learn how to breed for even greater nutritional value. Or imagine understanding how to manipulate the genes of the poppy plant so we could develop non-addictive morphine and other opiates."

Now dePamphilis and his colleagues have leveraged the success of the Floral Genome Project to create a successor, the newly-funded Ancestral Angiosperm Genome Project. Through this new project, he and collaborators at Washington University, the University of Arizona, the University of Florida, and the University of Georgia hope to "greatly expand the set of genetic data available for the early angiosperms."

Notes dePamphilis, "We';ve focused on just five of the species of special biological and economic interest from the Floral Genome Project- Amborella , water lily or Nympheaceae, yellow poplar or Liriodendron tulipifera, Dutchman's pipe or Aristolochia, and avocado or Persea americana -and we are expanding the collection of gene sequences by orders of magnitude by using next generation ultra-high throughput DNA sequencing technology." These new sequencing machines allow researchers to sequence genomes more affordably-and more than one thousand times faster-than ever before, he adds. " Penn State was an early adopter of one of the most powerful new instruments available-and this has dramatically changed the pace at which science can be done, including our own work in the AAGP."

"The analogy I like to use," says dePamphilis with a grin, "is the Hubble space telescope. The farther you can see, the further back in time you're looking. Some of the organisms we're examining have relatively slow rates of evolution, which means we can peer farther back in time to recover what the plant's ancestor was like. That's the goal: to look as deeply as we can into the genome to accurately reconstruct the detailed genetic history of the flower and other traits in plants.

Claude dePamphilis, Ph.D., is professor of biology in the Eberly College of Science and a faculty affiliate of the Huck Institutes of the Life Sciences, as well as principal investigator for the Ancestral Angiosperm Genome Project; cwd3@psu.edu. Other Penn State faculty collaborating on the project include Hong Ma, Ph.D., Naomi Altman, Ph.D. and John Carlson, Ph.D.